This proposal brings together the expertise of an accomplished team of researchers to complete the design and documentation necessary for implementing a first-in-human phase I/II translational trial, FDA approved recently FOA: PAR-13-150. It will evaluate the safety and efficacy of performing bilateral orthotopic lung transplantation (BOLT) followed by CD3+/CD19+-depleted bone marrow transplantation (BMT) from the same cadaveric, partially HLA-matched donor in primary immunodeficiency (PID) patients with pulmonary failure. The first human subject to have undergone this therapy has been off immunosuppressive therapy (IST) for >22 months with entirely donor-derived immunity and hematopoiesis. Importantly, in rat models of lung and marrow transplantation, stable mixed chimerism is sufficient to achieve tolerance. We propose to complete the design of a series of ancillary studies. First, we want to demonstrate the correction of the underlying immune deficit of each subject from donor-derived immune cells. Additionally, we propose to develop the portfolio of studies ready to test the following three hypotheses. We hypothesize 1) that in subjects with T cell defects, lymphocytes from the lungs may contribute to pathogen specific immunity prior to BMT; 2) that planned withdrawal of IST can be achieved not only in full donor chimerism but also in subjects with mixed chimerism; 3) that tolerance will develop differently in subjects engrafting with full donor T cell chimerism, where we predict that the donor stem cell derived T cell repertoire will lack host-reactive cells, in contrast with those subjects who exhibi mixed T cell chimerism. Here peripheral regulation would extinguish clonal alloreactivity. Aim I. Establish the research team and develop manuals of operation for the phase I/II clinical trial A. Clinical research process: Finalize statistical analysis plan, satisfy all necessary regulatory requirements to conduct the research study, establish data safety monitoring plan, training plans, CRFs, QC/audit procedures. B. Laboratory based studies: Finalize the team of collaborators, satisfy all necessary regulatory requirements to conduct ancillary studies, establish a manual of operations for specimen collection, archive, and analysis. Aim II. After team discussions, propose the portfolio of scientific assays and studies to investigate the evolution of immunity and the contribution attributable to donor cells during the planned U01 study. Each unique and distinct PID disease will be studied for both systemic and mucosal /pulmonary immunity. A. Develop the appropriate immune panels specific for PID disease categories, develop the portfolio of pulmonary pathogen-specific assays to characterize global and pathogen-specific immunity and to demonstrate the evolution of each immune deficiency disease to eventual immune competence. B. Propose the optimized portfolio of pathogen-specific mucosal and parallel systemic immunity assays. Aim III. After team discussions, propose the portfolio of immunological studies for the analysis and characterization of donor-host recognition/alloreactivity, and mechanism(s) of immune tolerance.